Sunday, May 5, 2013

Do Genes Switch Between Opposing DNA Strands For Adaptive Purposes?

As Luck Would Have it

In recent decades biologists have discovered that organisms possess a variety of adaptation mechanisms far more sophisticated than ever imagined. Some of these mechanisms are regulatory in that they influence which genes are used at a given time. Other mechanisms change the genes themselves by mutating the DNA sequences. These adaptive mutations respond to the current environmental challenge and such findings contradict contemporary evolution’s view that mutations are blind to need and are preserved only by the action of natural selection. Now, new research suggests yet another adaptive mutation mechanism.

The DNA double helix consists of two long strands wrapped around each other. Protein-coding genes can be on either strand, but one strand is more prone to mutations. This is because on that strand the DNA copying (replication) machine and the gene copying (transcription) machine move in opposing directions, and so head-on confrontations can occur. The new paper makes good arguments that these confrontations result in a higher mutation rate for genes on that strand.

Yet there are many genes on the “head-on” DNA strand. Why would that be? The new paper provides multiple evidences that not only these genes have incurred more mutations than normal, but that those mutations have often been helpful. That is, those mutations often have been adaptive.

So the paper hypothesizes that those genes are in the “head-on” orientation for good reason. They were genes that needed more mutations. The authors hypothesize a “replication–transcription conflict-mediated mutagenesis” strategy where genes that the organism particularly needs to modify are in the “head-on” DNA orientation.

This new hypothesis is not without its questions. For instance, while the “head-on” genes seem to reveal elevated levels of adaptive mutations, they do not show higher levels of mutations that do nothing to the protein’s amino acid sequence (the so-called synonymous mutations). Synonymous mutations are normally taken to reflect the underlying mutation rate. So if the mutation rate is higher due to a “head-on” orientation, then one would expect the synonymous mutation rate to be higher. That is standard evolutionary reasoning.

Another question is how and why do the genes switch from one DNA strand to the other, in the first place? In other words, this new strategy requires that genes switch from one strand to the other at some regular frequency. Whatever the mechanism, it must perform this switching at a rate that is not too low (or else very few genes would ever switch and evolutionary experimentation would be impossible) and not too high (or else the distribution between strands would be more random).

Finally there is, once again, the issue of serendipity. Under this new hypothesis evolution must have created a gene strand switching mechanism with an appropriate frequency. Such a mechanism would not provide any fitness improvement immediately. Instead the mechanism would set about switching, at random, genes from the strand they are on to the opposing strand.

And any such switches would also fail to provide fitness improvement immediately. But over time, some switches would help when certain genes undergo higher mutation rates. All of this means that evolution would have to create a sophisticated mechanism that only much later would provide benefit.

A typical explanation is that the new mechanism was simply a result of the combining of existing parts that were “lying around.” But this does nothing to reduce the serendipity involved. The bottom line here is that the new evidence forces evolutionary theory to take on even more complexity and serendipity. Evolution creates evolution.

37 comments:

These articles demonstrate over and over what Moronton has admitted. Naturalistic UCA research has nothing to do with probability. This is why plausibility has nothing to do with it. And this is why evidence has nothing to do with it. It's ASSUMED to be true. The rest is just explaining it with ad-hoc positing.

Unfortunately, such explanation IS subject to probabilistic analysis in some minimal way. An ad-hoc explanation for a given instance of biological variation inconsistent with all SA scenarios and non-genealogical scenarios has a humanly-assignable probability of at most 1/2 (to say otherwise is to be completely arbitrary in a partisan fashion). Thus, all millions of such ad-hoc posited causes/effects each have at most a non-arbitrarily-assignable probability of at most 1/2. Thus, the probability of naturalistic UCA on this approach is 1/2 raised to the power of however many millions of such events are posited to have occurred. We're talking a VERY low probability. And that equates to a VERY low plausibility.

How many assumptions are required to imply other scenarios? More or less than the millions required for naturalistic UCA? Prove it.

It's a good thing that the Creationist, fundamentalist Christians dim-bulbed their way into the whole Scientific Revolution thing, then. Too bad they weren't real scientists.

And seeing as how nobody considered slavery to be kinda mean until those same dim-bulbs very gradually abolished it over centuries...I'm not sure why you think 150 years is a particularly long time for a bad idea to stick around.

Long time ago, molecules accidentally assembled themselves into nano machines. Gamma ray smashed into one of the machine's molecular components and holy mama! nano machine worked little better. Gamma ray decided it was good and it won't smash that same component any more, instead it smashed another one and holy mama! nano machine worked even better....

"Evolution, Second Edition is a comprehensive treatment of contemporary evolutionary biology that is directed toward an undergraduate audience. It addresses major themes including the history of evolution, evolutionary processes, adaptation, and evolution as an explanatory framework at levels of biological organization ranging from genomes to ecological communities. Throughout, the text emphasizes the interplay between theory and empirical tests of hypotheses, thus acquainting students with the process of science. Teachers and students will find the list of important concepts and terms in each chapter a helpful guide, and will appreciate the dynamic figures and lively photographs. The content of all chapters has been updated. Contributors Scott V. Edwards and John R. True have once again provided authoritative chapters on, respectively, Evolution of Genes and Genomes and Evolution and Development, two of the most rapidly developing subjects in evolutionary biology. A final chapter on Evolutionary Science and Creationism treats such topics as the nature of science and the practical applications of evolutionary biology."

. An hypothetical question, if tomorrow the Mars rover found scientific proof of life , would the emergence of life from a merely natural mechanism be , more likely, less likely, or no difference? It Cassini detects life on one of the moons of Saturn, more,less or no difference?

Just curious, I will give you the report on the star viewing off the clock.

I think solar system should be "polluted" by extremophile life forms from Earth. They could be knocked out by massive bombardment Earth endured in a distant past. Environment of vacuum, absolute zero and high radiation would test limits of their survivability.

Maybe we should release some of extremophiles onto Mars soil and let them terraform for five hundred million years. By then we will need a new planet, Sun will become big enough to overheat the Earth and the Moon will get far enough so the Earth axis will destabilize.

TWT: Hey jeff and bpragmatic, will you please provide your detailed, scientific explanation for the diversity of life, with supporting evidence?

J: Why should I be able to do that when no one else has been able to? Neither you nor anyone else on this forum has ever provided one iota of evidence for naturalistic UCA.

Evidence is a relative concept. A set of assumptions and/or data only serves as evidence for a claim as compared to another set of assumptions and relevant data for a competing claim. To say a claim is evidenced in a non-relative way is to say it is SELF-evident, which is to say it is intuitive. Self-evident beliefs, like the law of non-contradiction, are not scientific hypotheses. They ground the very possibility and intelligibility of science.

In this case, the options for the origins of biological entities/properties are:

1) myriads of scenarios of purely naturalistic UCA,

2) myriads of scenarios of UCA that are NOT purely naturalistic,

3) myriads of scenarios of purely naturalisitc SA,

4) myriads of scenarios of SA that are NOT purely naturalistic,

and

5) kazillions of non-genealogical scenarios.

To say that any one of them is indicated by the data while the others aren't, or that one is MORE indicated than others, you have to state the relation the data holds to the assumptions of the explanatory theory that renders that "indication" true per your claim.

Not one person on this forum has any clue how to do that, seemingly. None of you naturalistic UCA'ists has ever demonstrated you know what evidence even is so as to apply it to the question rationally. Because you're sure not using the normal criteria of parsimony, etc, to do the comparison.

Oh sure, there are those who are so confused they think a handful of assumptions implies specific UCA lineages when really millions of ad-hoc assumptions are required. But that's because you and yours apparently are literally clueless as to how the hypothetico-deductive method works.

For someone who bemoans the lack of civility ,you seem to feel no need to heed your own advice. Your claim is a variation of the cosmological argument. And philosophers have been considering it for centuries. Alas they didn't consult you and save their time.

Is it natural in our universe for something to not have a cause?

That is the basis of science though quantum indeterminacy is possibly in conflict with our experience at the macro level

No its not.

Your expertise speaks for itself.

Its beyond (super) what we experience

Are you now saying that all supernatural stuff is Uncaused by definition?

You either invoke infinite regress which in and of itself is a supernatural appeal

Unless an Uncaused Cause is finite, an infinite regress is a possibilty.

you say the universe has at least one cause that is totally uncaused that has no explanation, reason or precursor - unlike everything else we have ever experienced in the natural world.

I agree.

Beyond is the meaning of the word "Super" and natural is what we see of the universe that everywhere has precursors - Supernatural.

"For someone who bemoans the lack of civility ,you seem to feel no need to heed your own advice."

I might have succumbed to watching the example you have set in previous threads but not entirely I don't think. I am pointed but not uncivil as I have seen here defended. I honestly believe you have not given it five minutes of thought. Its that clear.

"Your claim is a variation of the cosmological argument. And philosophers have been considering it for centuries. Alas they didn't consult you and save their time."

ah the old because an argument has been presented before we can pretend it has been rebutted to sidestep it gambit.

"That is the basis of science though quantum indeterminacy is possibly in conflict with our experience at the macro level"

Sorry This will not save your logic. Science can only tell us about things occurring within our present spacetime. IF you claim otherwise then you are back appealing to the supernatural. Though it is popular you cannot side step the issue by explaining that the cause of spacetime is a phenomenon that we observe taking place only within Spacetime. You are bucking up against both the absurd and the supernatural again just as I told you you would.

I know that people such as yourself believe quantum realities save you from the messiness of the first cause but you are deluded (Krauss being the leader of the deluded). You are still both left with an uncaused cause and given infinity you would be left with a universe where everything is not only possible but must already have actuated (poor krauss believes that the everything would somehow preclude God but he hasn't thought about it for five minutes either) . Unfortunately a supreme being would be one of those everythings so we would be left with a certainty of God's existence and given the nature of infinity a God of infinite origins.

THink about if for five minutes

"Unless an Uncaused Cause is finite, an infinite regress is a possibilty."

I'm sorry but you just completely confused yourself. An infinite regress BY DEFINITION demands an uncaused cause so you are still stuck with the supernatural premise of something (and everything that exists) having no ultimate explanation reason or cause in defiance of everything we see in our universe. AN infinite regress would have no beginning whatsoever and therefore no ultimate cause. Infinite moving forward in time has no end moving back in time it has no beginning.

Furthermore every ability this infinite entity has would have equally no explanation but merely would be for the reason that it is ( incredibly close to The Old testament name for God given to moses merely as "I AM that I am ).

This as you see gets you nowhere again but looking at the inevitability of the supernatural.

"Are you now saying that all supernatural stuff is Uncaused by definition?"

No I am not. I am saying that anytime you appeal to something outside of the universe we see and observe you are invoking metaphysics and the supernatural. I am breaking down the meaning of Supernatural. Super - meaning beyond Natural meaning what we see and observe in this universe.

It really is inescapable but its not something that materialists want to look at and in particularly not atheists because it eviscerates one of their treasured props that the very idea of the supernatural is absurd.

The fact that both sides end up at the same place makes it inevitable that the only difference between them logically is not in believing in the supernatural but as to whether the supernatural possesses logic and intelligence. It can be argued that that is the ONLY real difference.

We know of nothing in this universe (and that includes quantum fields, virtual particles or whatever you wish) that does not originate from something or somewhere else.

"If the argument is correctly deployed it is convincing. The question is whether you achieved that."

IF the conclusion is escapable on a logical ground I am open to hearing it. If not it has been achieved on the merits not whether this or that human being chooses to accept it. I dont know which you will choose but just stating the facts of that.

Personally, I define naturalism as the study of the nature of things. Anything which has a nature which distinguishes it from all other things is part of the natural order, whether in this universe or some other. This makes the concept of supernatural effectively redundant since ghosts or even gods, if they exist as such, have their natures and are thus part of the natural world.

Say - isn't Hunter the guy who took a picture of a wolf, reversed it, altered the contrast, then claimed it was a Thylacine, then compared it to a picture of a wolf and declared that they look so much alike that evolution can't explain it?

And then, after getting caught, said it was all a 'mistake'? And there are people DEFENDING this guy? Amazing...

I don't know (the real?) Sam Harris. Is that what happened? Why is it not plausible that that would be a mistake?

Here's Hunter's explanation:"you *are* pointing out a mistake in my graphics. Both wolf images were straight off the web, and in my hasty collection of marsupial and placental examples I accidentally got a marsupial wolf graphic confused as a placental. Yes it was a dumb mistake, but it was not at all important to my uncontroversial point, which was that in biology there are many convergences."

Do you have any evidence that your narrative is the right one, or do you uncharitably assume the very worst about people with whom you disagree?

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Cornelius G. Hunter is a graduate of the University of Illinois where
he earned a Ph.D. in Biophysics and Computational Biology. He is
Adjunct Professor at Biola University and author of the award-winning Darwin’s God: Evolution and the Problem of Evil. Hunter’s other books include Darwin’s Proof, and his newest book Science’s Blind Spot
(Baker/Brazos Press). Dr. Hunter's interest in the theory of evolution
involves the historical and theological, as well as scientific, aspects
of the theory. His website is http://www.darwins-god.blogspot.com/